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- PDB-1zl9: Crystal Structure of a major nematode C.elegans specific GST (CE01613) -

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Basic information

Entry
Database: PDB / ID: 1zl9
TitleCrystal Structure of a major nematode C.elegans specific GST (CE01613)
Componentsglutathione S-transferase 5
KeywordsTRANSFERASE / glutathione transferase / C.elegans
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / glutathione metabolic process / innate immune response
Similarity search - Function
Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal ...Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE / Probable glutathione S-transferase 5
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsKriksunov, I.A. / Liu, Q. / Schuller, D.J. / Campbell, A.M. / Barrett, J. / Brophy, P.M. / Hao, Q.
CitationJournal: To be Published
Title: Crystal structure of a major nematode C.elegans specific GST (CE01613)
Authors: Kriksunov, I.A. / Liu, Q. / Schuller, D.J. / Campbell, A.M. / Barrett, J. / Brophy, P.M. / Hao, Q.
History
DepositionMay 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 14, 2011Group: Non-polymer description
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: glutathione S-transferase 5
B: glutathione S-transferase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1734
Polymers46,5592
Non-polymers6152
Water8,269459
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-11 kcal/mol
Surface area19170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.960, 88.272, 93.596
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein glutathione S-transferase 5 / GST class-sigma


Mass: 23279.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: gst-5, CE01613 / Plasmid: pET23d(Novagen) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 pLysS / References: UniProt: Q09596, glutathione transferase
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 459 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 65% MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.916 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 7, 2003 / Details: RH-COATED SI MONOCHROMATIC MIRRORS
RadiationMonochromator: RH-COATED SI MONOCHROMATIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. all: 33787 / Num. obs: 33450 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 28.3
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 5.4 / Num. unique all: 1636 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
Adxvdata processing
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TW9

1tw9


Resolution: 2.01→25 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.901 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.144 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20912 867 2.6 %RANDOM
Rwork0.15069 ---
all0.1798 32715 --
obs0.1522 32388 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.599 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å20 Å2
2--0.89 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.01→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3298 0 40 459 3797
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0223428
X-RAY DIFFRACTIONr_bond_other_d0.0020.023020
X-RAY DIFFRACTIONr_angle_refined_deg1.7481.9514630
X-RAY DIFFRACTIONr_angle_other_deg1.15637052
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.815412
X-RAY DIFFRACTIONr_chiral_restr0.2860.2476
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023832
X-RAY DIFFRACTIONr_gen_planes_other0.0150.02742
X-RAY DIFFRACTIONr_nbd_refined0.220.2750
X-RAY DIFFRACTIONr_nbd_other0.260.23321
X-RAY DIFFRACTIONr_nbtor_other0.090.21819
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2339
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2440.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.221
X-RAY DIFFRACTIONr_mcbond_it1.1461.52056
X-RAY DIFFRACTIONr_mcangle_it2.05723278
X-RAY DIFFRACTIONr_scbond_it3.39231372
X-RAY DIFFRACTIONr_scangle_it5.1944.51352
LS refinement shellResolution: 2.006→2.058 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.203 59
Rwork0.156 2249
obs-2249

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